LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
Reading data file ...
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     5 = max # of 1-2 neighbors
    10 = max # of 1-3 neighbors
    16 = max # of 1-4 neighbors
    20 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.040 seconds

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT


neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
Finding SHAKE clusters ...
    1250 = # of size 2 clusters
       0 = # of size 3 clusters
     250 = # of size 4 clusters
       0 = # of frozen angles
  find clusters CPU = 0.001 seconds

compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.38201098
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.032593379
  estimated relative force accuracy = 9.8153994e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 103823 64000
Generated 10 of 66 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.31 | 42.31 | 42.31 Mbytes
   Step         TotEng         KinEng          Temp          PotEng         E_bond        E_angle        E_dihed        E_impro         E_vdwl         E_coul         E_long         Press          Volume       c_cTEMP[1]     c_cTEMP[2]  
         0   11086.38       2910.7282      202.07402      8175.6516      6565.4851      20.333365      1.0706727e-06 -3299.85        4972.8631      1306116.7     -1306199.8      40273.655      48631.318      314.89553      3.1777821    
        50   3563.376       4630.6335      321.47649     -1067.2575      735.72624      604.7866       689.14825     -3277.411       815.58186      1306088.7     -1306723.8      17813.41       48631.318      503.82692      0.0087121566 
       100   3327.4747      4395.1102      305.12556     -1067.6355      597.93699      651.62626      945.41506     -3267.2851      584.5884       1306135.9     -1306715.8      17407.333      48631.318      478.20165      0.0075989631 
       150   3036.9098      4740.229       329.08504     -1703.3193      558.65575      619.91293      658.8068      -3278.7837      285.12479      1306173       -1306720        18448.252      48631.318      515.75272      0.006321922  
       200   2697.9601      4559.3437      316.52728     -1861.3836      522.09846      593.89117      754.61436     -3273.49        87.660605      1306183.9     -1306730        17888.928      48631.318      496.07134      0.0068710202 
       250   2348.758       4410.5839      306.1998      -2061.8259      506.05492      575.35161      715.55052     -3276.3261     -18.364562      1306177.3     -1306741.4      11592.029      48631.318      479.8855       0.0071745639 
       300   2019.8267      4040.1403      280.48217     -2020.3136      604.31243      641.66669      693.9379      -3278.5312     -115.73614      1306183.2     -1306749.1      3631.372       48631.318      439.57982      0.0069892966 
       350   1699.5126      3944.9847      273.8761      -2245.4721      452.07861      638.06481      658.791       -3279.6053     -157.07617      1306196.9     -1306754.6      13544.381      48631.318      429.2269       0.0062876757 
       400   1399.2967      3726.0964      258.68003     -2326.7997      457.92465      621.44729      639.39889     -3279.2395     -188.85919      1306185.4     -1306762.8      10792.249      48631.318      405.41116      0.0059345238 
       450   1120.5239      3518.3436      244.25703     -2397.8197      519.49329      584.65761      646.36683     -3278.6685     -289.59888      1306184.1     -1306764.2      2755.548       48631.318      382.80701      0.0055711034 
       500   868.02119      3359.8788      233.25579     -2491.8576      460.74393      581.49501      581.01733     -3281.5544     -252.20173      1306184.3     -1306765.7      6120.3719      48631.318      365.56522      0.0058762213 
       550   637.01506      3214.9508      223.19432     -2577.9358      431.81989      578.87404      540.94038     -3281.5337     -266.36059      1306182.8     -1306764.5      8622.4402      48631.318      349.79647      0.0058598291 
       600   418.04365      3113.4054      216.14465     -2695.3618      430.4641       538.68145      522.24584     -3283.456      -311.88142      1306174.3     -1306765.8      7068.9206      48631.318      338.74786      0.0059573645 
       650   218.59262      2930.8426      203.47043     -2712.2499      514.4777       514.28332      551.52555     -3282.0904     -405.37359      1306164.5     -1306769.5     -13.588458      48631.318      318.88467      0.0052673284 
       700   45.22755       2830.1426      196.47945     -2784.915       451.11592      498.26416      541.18813     -3282.1428     -375.95195      1306157.1     -1306774.4      3947.6667      48631.318      307.92723      0.0068028221 
       750  -114.28083      2798.3147      194.26983     -2912.5955      412.75789      503.28763      481.32131     -3284.3411     -393.53933      1306147       -1306779.1      7143.3412      48631.318      304.46459      0.0061605332 
       800  -263.63975      2694.8105      187.08417     -2958.4502      455.68389      487.49661      476.86536     -3284.3133     -451.95749      1306144.9     -1306787.2      1185.8632      48631.318      293.2031       0.0058210781 
       850  -397.71728      2559.1905      177.66891     -2956.9078      458.83777      481.22598      478.31207     -3284.068      -437.26349      1306138.6     -1306792.6      346.83         48631.318      278.44728      0.0054927474 
       900  -515.18203      2544.8732      176.67494     -3060.0552      395.00614      457.58883      446.68517     -3285.4849     -423.56152      1306145       -1306795.3      3712.8756      48631.318      276.88841      0.0074070031 
       950  -617.28486      2451.1723      170.16986     -3068.4571      383.64784      446.59655      434.46259     -3285.1347     -391.59088      1306142.3     -1306798.7      5429.1959      48631.318      266.69431      0.0057497879 
      1000  -703.15156      2334.8372      162.09343     -3037.9888      424.35501      462.20937      451.80779     -3284.3803     -426.53395      1306133.9     -1306799.3      1137.5765      48631.318      254.03678      0.0053919739 
      1050  -771.1803       2303.8356      159.94118     -3075.0159      426.21866      436.50653      435.10098     -3285.1938     -411.13895      1306125.6     -1306802.1      1636.9108      48631.318      250.6628       0.0069363905 
      1100  -822.71796      2283.421       158.52392     -3106.1389      376.68164      447.77457      418.45912     -3286.5918     -377.48415      1306118.9     -1306803.8      4760.5562      48631.318      248.44134      0.0074028548 
      1150  -857.05531      2259.0862      156.8345      -3116.1415      400.32029      431.65761      457.68017     -3285.1977     -430.49179      1306115.8     -1306805.9      3194.3289      48631.318      245.79381      0.0070649678 
      1200  -875.50952      2238.2653      155.38904     -3113.7749      445.38688      460.96756      432.10434     -3285.4239     -472.45904      1306114.7     -1306809       -653.39006      48631.318      243.52837      0.0071469368 
      1250  -880.37208      2294.6859      159.30598     -3175.058       411.3601       444.73283      420.06245     -3286.0365     -458.04674      1306104.4     -1306811.5      945.91365      48631.318      249.66448      0.011861435  
      1300  -871.30319      2284.2307      158.58013     -3155.5339      404.98364      441.75152      426.34826     -3285.4859     -424.7993       1306094.9     -1306813.2      4406.5059      48631.318      248.48569      0.084495122  
      1350  -816.6719       2325.9605      161.47717     -3142.6324      697.11308      442.49743      431.19394     -3285.786      -450.28363      1305835.9     -1306813.3      593.39946      48631.318      251.41019      2.9314998    
      1400  -794.27273      2263.5095      157.14159     -3057.7823      645.48778      466.21647      446.22237     -3285.1824     -420.66373      1305903.9     -1306813.7      1386.1404      48631.318      245.20614      1.8904447    
      1450  -776.11247      2287.6318      158.81625     -3063.7443      427.03376      479.09978      439.69106     -3285.9534     -395.11778      1306087.6     -1306816.1      2937.0883      48631.318      248.86892      0.061272681  
      1500  -725.47214      2371.409       164.63239     -3096.8812      390.04047      464.29754      446.92729     -3284.7807     -393.16487      1306095.4     -1306815.6      3544.5027      48631.318      258.01242      0.011592014  
      1550  -671.47482      2315.9323      160.78098     -2987.4071      457.0407       500.27004      464.7666      -3284.9303     -401.00215      1306091.7     -1306815.3      2052.1763      48631.318      251.97754      0.0094582549 
      1600  -618.83791      2449.0828      170.0248      -3067.9207      425.47283      474.66994      472.00022     -3284.3677     -430.3313       1306091.3     -1306816.6      441.37381      48631.318      266.46213      0.014272902  
      1650  -567.8145       2425.2171      168.36796     -2993.0316      421.03479      511.22291      463.22254     -3285.0375     -377.21724      1306088.4     -1306814.7      5198.4421      48631.318      263.83108      0.074819853  
      1700  -502.4044       2441.8219      169.52073     -2944.2263      642.73496      512.85266      490.47499     -3283.9752     -417.40246      1305928.8     -1306817.7      1140.4596      48631.318      264.5182       2.0473498    
      1750  -459.54561      2499.1118      173.49801     -2958.6574      678.90861      505.20327      484.78338     -3284.6278     -384.25437      1305862.2     -1306820.8      1527.9678      48631.318      270.1077       3.1817914    
      1800  -471.12805      2476.216       171.9085      -2947.3441      442.50898      530.45109      474.05658     -3284.0975     -371.94385      1306084.3     -1306822.6      3393.1525      48631.318      269.36338      0.10403847   
      1850  -462.77008      2536.8048      176.1148      -2999.5749      437.10918      525.0048       474.11272     -3283.7914     -422.27406      1306091.6     -1306821.3      1628.4329      48631.318      276.00519      0.01682653   
      1900  -469.85317      2469.0429      171.41051     -2938.896       446.83192      531.60209      496.09807     -3284.2291     -395.30851      1306085.7     -1306819.6      3116.6217      48631.318      268.63366      0.014626031  
      1950  -491.03803      2445.6922      169.78942     -2936.7302      457.78458      527.28677      470.17877     -3283.9669     -391.9058       1306101.8     -1306817.9      1123.2076      48631.318      266.09057      0.018929256  
      2000  -518.31769      2418.3069      167.88822     -2936.6246      415.92254      536.70542      480.47837     -3283.7852     -363.54193      1306096.3     -1306818.7      4473.3825      48631.318      263.04508      0.13496381   
Loop time of 41.8393 on 1 procs for 2000 steps with 5500 atoms

Performance: 2.065 ns/day, 11.622 hours/ns, 47.802 timesteps/s, 262.911 katom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.899     | 27.899     | 27.899     |   0.0 | 66.68
Bond    | 1.967      | 1.967      | 1.967      |   0.0 |  4.70
Kspace  | 8.6235     | 8.6235     | 8.6235     |   0.0 | 20.61
Neigh   | 1.0246     | 1.0246     | 1.0246     |   0.0 |  2.45
Comm    | 0.16775    | 0.16775    | 0.16775    |   0.0 |  0.40
Output  | 0.0029905  | 0.0029905  | 0.0029905  |   0.0 |  0.01
Modify  | 2.1138     | 2.1138     | 2.1138     |   0.0 |  5.05
Other   |            | 0.04026    |            |       |  0.10

Nlocal:           5500 ave        5500 max        5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          15317 ave       15317 max       15317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.30289e+06 ave 1.30289e+06 max 1.30289e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1302891
Ave neighs/atom = 236.88927
Ave special neighs/atom = 15.636364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:41
